A Complete Guide to Mass Spectrometers

Mass spectrometers are one of the key tools in the analytical sciences and we provide a complete guide to them in this blog post.

Mass spectrometers are one of the key tools in the analytical sciences. With the ability to perform quantitative and qualitative analysis on a huge variety of sample types, mass spectrometers have found use in nearly every sector of industry and research.
Mass spectrometry can be used as a standalone technique or as a ‘hyphenated’ method, where it is combined with another separation technique like liquid chromatography or gas chromatography. Using hyphenated methods with mass spectrometers or tandem mass spectrometers for MS/MS makes it possible to obtain very detailed information on even highly chemically complex samples, like tissues, bloods, and soils.1 
Other recent developments in mass spectrometry that have helped extend the range of applications are machine learning-based methods for data analysis that have made it possible to analyze significantly more complex datasets, such as for metabolomics.2 Another experimental development is advances in ambient ionization methods that have moved mass spectrometry to be a real-time sampling method ideal for performing rapid measurements with no need for sample preparation.3
All of the chemical identification work that can be done with mass spectrometry relies on a measurement of the mass-to-charge ratio of the intact molecule and/or fragment ions. Depending on the ionization conditions for the sample, a molecule will have a characteristic fragmentation pattern in the mass spectrum that can be used to identify it. 
Accurate mass information can be used not just for compound identification but also for processes such as carbon dating, where the abundance of a radioactive isotope of carbon can be used to estimate the age of the sample. Achieving good mass separation and resolution in a mass spectrometer is critical to realizing its full measurement capabilities. So how does the mass spectrometer instrumentation achieve this? 

How do they work?

    Mass spectrometers ionize samples using a choice of ion sources, such as electron ionization (EI) or matrix-assisted laser desorption ionization (MALDI). Afterward, the charged ions are accelerated into the analyzer by an electrical field, where their paths begin to vary due to their differences in mass. While there are a variety of analyzers that can be used, time-of-flight (TOF) analyzers are the simplest to explain in that they use the kinetic energy equation KE=(½)mv^2. Since each ion is accelerated with the same kinetic energy, mass and velocity are the only variables. Hence, smaller ions travel faster through a field-free drift region while heavy ions travel slower. Measuring the time-of-flight of the ion subsequently gives the mass-to-charge (m/z) ratio, which helps distinguish between ions of different masses, thus helping to identify the chemical constituents of a sample.

    It is also worth highlighting the impact of different ionization sources on sample integrity. Ionization can be classified as ‘soft’ or ‘hard’ depending on how much fragmentation they induce in a sample. EI is considered a hard ionization technique as it uses such high energy that samples are not only ionized but also broken into fragments. However, these fragments can provide valuable information about an analyte’s molecular structures, particularly when compared against established mass spectral libraries. Therefore, hard ionization is a useful method for producing reproducible fragmentation patterns. By contrast, a soft ionization technique like MALDI provides minimum fragmentation, which is preferable when the intact molecular weight of the sample is of interest.

    JEOL’s Mass Spectrometers 

    JEOL is one of the world's leading instrument designers and manufacturers in mass spectrometry. JEOL offers an extensive range of mass spectrometry instrumentation, including the hyphenated AccuTOF GCxGC-MS and AccuTOF LC-Express as well as the tandem SpiralTOF MALDI TOF/TOF.

    No matter what the application, JEOL has the right mass spectrometer for you and can help advise on what instrumentation is best suited for your application.
    Combined with world-leading software, JEOL’s cutting-edge instruments will help you achieve better sample throughput, acquisition times, and mass spectrometry performance. Contact JEOL today to find out how their instrumentation could benefit you.


      1. Neagu AN, Jayathirtha M, Baxter E, Donnelly M, Petre BA, Darie CC. Applications of Tandem Mass Spectrometry (MS/MS) in Protein Analysis for Biomedical Research. Molecules. 2022 Apr 8;27(8):2411. doi: 10.3390/molecules27082411. PMID: 35458608; PMCID: PMC9031286.
      2. Liebal, U. W., Phan, A. N. T., Sudhakar, M., Raman, K., & Blank, L. M. (2020). Machine Learning Applications for Mass Spectrometry-based Metabolomics. Metabolites, 10, 243.
      3. Feider, C. L., Krieger, A., Dehoog, R. J., & Eberlin, L. S. (2019). Ambient Ionization Mass Spectrometry: Recent Developments and Applications. Analytical Chemistry, 91, 4266–4290.


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